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<div class="main">
<div class="sidemenu"><div class="sidemenu_head">Links</div>
	<div class="sidemenu_body"><ul><li><a href="#masthead">Top of page</a></li>
	<li><a href="#run_stats">VEP run statistics</a></li>
	<li><a href="#gen_stats">General statistics</a></li>
	<li><a href="#var_class">Variant classes</a></li>
	<li><a href="#var_cons">Consequences (most severe)</a></li>
	<li><a href="#consequences">Consequences (all)</a></li>
	<li><a href="#coding">Coding consequences</a></li>
	<li><a href="#sift">SIFT summary</a></li>
	<li><a href="#polyphen">PolyPhen summary</a></li>
	<li><a href="#chr">Variants by chromosome</a></li>
	<li><a href="#protein">Position in protein</a></li></ul></div></div><div class='main_content'><h3 id="run_stats">VEP run statistics</h3><table class="stats_table"><tr><td>VEP version (API)</td>
	<td>74 (74)</td></tr>
	<tr><td>Cache/Database</td>
	<td>/scratch1/vax/homo_sapiens/74</td></tr>
	<tr><td>Species</td>
	<td>homo_sapiens</td></tr>
	<tr><td>Command line options</td>
	<td><pre>--config /share/apps/myourshaw/vax/vep.ini --input_file /home/myourshaw/lab/pypeline/20_17437045_C_T.vcf --output_file /home/myourshaw/lab/pypeline/20_17437045_C_T.vcf.vax</pre></td></tr>
	<tr><td>Start time</td>
	<td>2014-05-29 12:06:48</td></tr>
	<tr><td>End time</td>
	<td>2014-05-29 12:08:57</td></tr>
	<tr><td>Run time</td>
	<td>129 seconds</td></tr>
	<tr><td>Input file (format)</td>
	<td>/home/myourshaw/lab/pypeline/20_17437045_C_T.vcf (VCF)</td></tr>
	<tr><td>Output file</td>
	<td>/home/myourshaw/lab/pypeline/20_17437045_C_T.vcf.vax <a href="/home/myourshaw/lab/pypeline/20_17437045_C_T.vcf.vax">[text]</a></td></tr></table><h3 id="gen_stats">General statistics</h3><table class="stats_table"><tr><td>Lines of input read</td>
	<td>2</td></tr>
	<tr><td>Variants processed</td>
	<td>1</td></tr>
	<tr><td>Variants remaining after filtering</td>
	<td>1</td></tr>
	<tr><td>Lines of output written</td>
	<td>4</td></tr>
	<tr><td>Novel / known variants</td>
	<td>0 (0.0%) / 1 (100.0%)</td></tr>
	<tr><td>Overlapped genes</td>
	<td>1</td></tr>
	<tr><td>Overlapped transcripts</td>
	<td>3</td></tr>
	<tr><td>Overlapped regulatory features</td>
	<td>1</td></tr></table><hr /><h3 id="var_class">Variant classes</h3><div id="var_class_pie"
	style="width: 800px; height: 200px">&nbsp;</div><div style="width: 800px; height: 200px"
	id="var_class_table">&nbsp;</div><hr /><h3 id="var_cons">Consequences (most severe)</h3><div style="width: 800px; height: 400px"
	id="var_cons_pie">&nbsp;</div><div id="var_cons_table"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="consequences">Consequences (all)</h3><div style="width: 800px; height: 400px"
	id="consequences_pie">&nbsp;</div><div id="consequences_table"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="coding">Coding consequences</h3><div style="width: 800px; height: 400px"
	id="coding_pie">&nbsp;</div><div id="coding_table"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="sift">SIFT summary</h3><div id="sift_pie"
	style="width: 800px; height: 200px">&nbsp;</div><div id="sift_table"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="polyphen">PolyPhen summary</h3><div id="polyphen_pie"
	style="width: 800px; height: 200px">&nbsp;</div><div id="polyphen_table"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="chr">Variants by chromosome</h3><div id="chr_bar"
	style="width: 800px; height: 200px">&nbsp;</div><div style="width: 800px; height: 200px"
	id="chr_table">&nbsp;</div><hr /><h3 id="chr_20">Distribution of variants on chromosome 20</h3><div id="chr_20_area"
	style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="protein">Position in protein</h3><div style="width: 800px; height: 200px"
	id="protein_bar">&nbsp;</div></div>
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